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  1. Research article

    Recognizing chemicals in patents: a comparative analysis

    Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER f...

    Maryam Habibi, David Luis Wiegandt, Florian Schmedding and Ulf Leser

    Journal of Cheminformatics 2016 8:59

    Published on: 28 October 2016

  2. Methodology

    Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry

    In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. T...

    Junaid Arshad, Alexander Hoffmann, Sandra Gesing, Richard Grunzke, Jens Krüger, Tamas Kiss, Sonja Herres-Pawlis and Gabor Terstyanszky

    Journal of Cheminformatics 2016 8:58

    Published on: 20 October 2016

  3. Research article

    Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance

    In a structure-based virtual screening, the choice of the docking program is essential for the success of a hit identification. Benchmarks are meant to help in guiding this choice, especially when undertaken ...

    Ludovic Chaput, Juan Martinez-Sanz, Nicolas Saettel and Liliane Mouawad

    Journal of Cheminformatics 2016 8:56

    Published on: 17 October 2016

  4. Software

    NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

    The concept of partial atomic charges was first applied in physical and organic chemistry and was later also adopted in computational chemistry, bioinformatics and chemoinformatics. The electronegativity equal...

    Tomáš Raček, Jana Pazúriková, Radka Svobodová Vařeková, Stanislav Geidl, Aleš Křenek, Francesco Luca Falginella, Vladimír Horský, Václav Hejret and Jaroslav Koča

    Journal of Cheminformatics 2016 8:57

    Published on: 17 October 2016

  5. Research article

    Evolution of DFT studies in view of a scientometric perspective

    This bibliometric study aims to analyze the publications in which density functional theory (DFT) plays a major role. The bibliometric analysis is performed on the full publication volume of 114,138 publicatio...

    Robin Haunschild, Andreas Barth and Werner Marx

    Journal of Cheminformatics 2016 8:52

    Published on: 5 October 2016

  6. Research article

    Computational methods for prediction of in vitro effects of new chemical structures

    With a constant increase in the number of new chemicals synthesized every year, it becomes important to employ the most reliable and fast in silico screening methods to predict their safety and activity profil...

    Priyanka Banerjee, Vishal B. Siramshetty, Malgorzata N. Drwal and Robert Preissner

    Journal of Cheminformatics 2016 8:51

    Published on: 29 September 2016

  7. Software

    Jmol SMILES and Jmol SMARTS: specifications and applications

    SMILES and SMARTS are two well-defined structure matching languages that have gained wide use in cheminformatics. Jmol is a widely used open-source molecular visualization and analysis tool written in Java and...

    Robert M. Hanson

    Journal of Cheminformatics 2016 8:50

    Published on: 26 September 2016

  8. Preliminary communication

    Mixtures, metabolites, ionic liquids: a new measure to evaluate similarity between complex chemical systems

    This communication deals with the scientific problem of evaluating the similarity between two chemical systems, each described by a finite discrete set of elements/members, which are in turn p-dimensional vectors...

    Andrea Mauri, Davide Ballabio, Roberto Todeschini and Viviana Consonni

    Journal of Cheminformatics 2016 8:49

    Published on: 22 September 2016

  9. Research article

    An ensemble model of QSAR tools for regulatory risk assessment

    Quantitative structure activity relationships (QSARs) are theoretical models that relate a quantitative measure of chemical structure to a physical property or a biological effect. QSAR predictions can be used...

    Prachi Pradeep, Richard J. Povinelli, Shannon White and Stephen J. Merrill

    Journal of Cheminformatics 2016 8:48

    Published on: 22 September 2016

  10. Database

    XMetDB: an open access database for xenobiotic metabolism

    Xenobiotic metabolism is an active research topic but the limited amount of openly available high-quality biotransformation data constrains predictive modeling. Current database often default to commonly avail...

    Ola Spjuth, Patrik Rydberg, Egon L. Willighagen, Chris T. Evelo and Nina Jeliazkova

    Journal of Cheminformatics 2016 8:47

    Published on: 15 September 2016

  11. Software

    Ligand-based virtual screening interface between PyMOL and LiSiCA

    Ligand-based virtual screening of large small-molecule databases is an important step in the early stages of drug development. It is based on the similarity principle and is used to reduce the chemical space o...

    Athira Dilip, Samo Lešnik, Tanja Štular, Dušanka Janežič and Janez Konc

    Journal of Cheminformatics 2016 8:46

    Published on: 7 September 2016

  12. Software

    Molmil: a molecular viewer for the PDB and beyond

    We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan an...

    Gert-Jan Bekker, Haruki Nakamura and Akira R. Kinjo

    Journal of Cheminformatics 2016 8:42

    Published on: 26 August 2016

  13. Research article

    An activity canyon characterization of the pharmacological topography

    Highly chemically similar drugs usually possess similar biological activities, but sometimes, small changes in chemistry can result in a large difference in biological effects. Chemically similar drug pairs th...

    Varsha S. Kulkarni and David J. Wild

    Journal of Cheminformatics 2016 8:41

    Published on: 19 August 2016

  14. Research article

    ILPC: simple chemometric tool supporting the design of ionic liquids

    Ionic liquids (ILs) found a variety of applications in today’s chemistry. Since their properties depend on the ions constituting particular ionic liquid, it is possible to synthetize IL with desired specificat...

    Maciej Barycki, Anita Sosnowska, Magdalena Piotrowska, Piotr Urbaszek, Anna Rybinska, Monika Grzonkowska and Tomasz Puzyn

    Journal of Cheminformatics 2016 8:40

    Published on: 19 August 2016

  15. Research article

    Large-scale ligand-based predictive modelling using support vector machines

    The increasing size of datasets in drug discovery makes it challenging to build robust and accurate predictive models within a reasonable amount of time. In order to investigate the effect of dataset sizes on ...

    Jonathan Alvarsson, Samuel Lampa, Wesley Schaal, Claes Andersson, Jarl E. S. Wikberg and Ola Spjuth

    Journal of Cheminformatics 2016 8:39

    Published on: 10 August 2016

  16. Research article

    bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming

    Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algo...

    Jun Gao, Qingchen Zhang, Min Liu, Lixin Zhu, Dingfeng Wu, Zhiwei Cao and Ruixin Zhu

    Journal of Cheminformatics 2016 8:38

    Published on: 11 July 2016

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